The ecological stoichiometric properties of desert soils determine nutrient availability and contribute to biodiversity and ecosystem stability. We obtained 1784 soil samples from 330 soil profiles distributed across the desert area of the Qinghai–Tibet Plateau (QTP). We measured the content of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) to elucidate the vertical patterns of soil stoichiometric characteristics and their driving factors. We found a unique vertical distribution of SOC and soil nutrients in the QTP desert ecosystem: the proportions of SOC and nutrient storage in the topsoil (0–20 cm) were the highest that have been reported to date, especially for the proportion of SOC, which reached 54 %. The vertical distributions of SOC and AN fit an exponential function (r = 0.247 and 0.249), TN fit a linear function (r = 0.115), and TP, AP, and AK fit a curvilinear function (r = 0.127, 0.175, and 0.103), indicating that soil components exhibited a depth-dependent distribution in the alpine desert ecosystem. With increasing soil depth, C:N and C:P decreased significantly, AN:AP first increased and then decreased, and AP:AK first decreased and then increased. The factors that influenced soil nutrients and stoichiometry differed between the topsoil (0–20 cm) and deep soil (20–100 cm) layers. In the topsoil (0–20 cm), vegetation and precipitation were the dominant factors for soil nutrients and stoichiometry, while topography and climate affected soil nutrients and stoichiometry indirectly by influencing vegetation growth. In the deep soil (20–100 cm), silt particles and precipitation were the dominant factors for soil nutrients and stoichiometry, but climate affected soil nutrients and stoichiometry indirectly, mainly by influencing soil texture. The inconsistencies of nutrient stoichiometric driving mechanisms in surface and deep soils contributed to a comprehensive understanding of soil stoichiometric properties at the profile scale of desert ecosystems.